Bowtie cant read my csfasta file !

[lakshmaa]

Hi everyone,

I have a color space fasta file and i have created the index files using bowtie-build. I ran bowtie using

/share/bin/bowtie/bowtie -a -v2 -C --sam -f 0604_refMrna_index GFP_plus_20091102_F3.csfasta

It complains of:
Error: reads file does not look like a FASTA file
Command: /share/bin/bowtie/bowtie -a -v2 -C --sam -f 0604_refMrna_index GFP_plus_20091102_F3.csfasta

Can anyone help me with this?

Thanks,
Abby

[Ben Langmead]

Hi Abby,

Could you please post the output of 'bowtie --version' (so we know exactly what version you're using) and give a snippet of the CSFASTA file that Bowtie's complaining about?

Thanks,
Ben

[lakshmaa]

Ben,

my csfasta file had

# Tue Nov 24 17:11:31 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/solid0171/solid0171_20091102/SarahS_mix
/results.01/primary.20091119193646015 --name=solid0171_20091102_SarahS_mix --tag=F3 --minlength=50 --mincalls=25 --prefix=T /dat
a/results/solid0171/solid0171_20091102/SarahS_mix/jobs/postPrimerSetPrimary.555/rawseq
# Cwd: /state/partition1/home/pipeline
# Title: solid0171_20091102_SarahS_mix
>1_32_39_F3
T1302221.231022221222222202022020222200022000022000

I was playing with this file and finally figured out that removing the commented lines make it work. Thank you. I have another quick question what options will help me get the position numbers where the reads map to ? right now i am using :

-C -f --sam --sam-nosq --al <filename> .

Thanks,
Abby

[Ben Langmead]

Hi Abby,

Oops, OK, I'll take a look at that. Comment lines *should* be handled gracefully, so that's a bug.

See the Bowtie manual (and, if more details is needed, the SAM specification) for how to interpret the SAM output columns. The name and offset for the reference aligned to are in the third and fourth columns respectively.

Thanks,
Ben

[lakshmaa]

Thank you !

Abby